Signatures within the esophageal microbiome are associated with host genetics, age, and disease

Study information

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incomplete

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

30558669

DOI Digital object identifier for electronic documents.

https://doi.org/10.1186/s40168-018-0611-4

URI

https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0611-4

Authors

Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR, Kaakoush NO

Journal

Microbiome

Year

2018

Keywords:

Community types, Esophagus, Metagenomics, Microbiota, Single nucleotide polymorphisms

BACKGROUND: The esophageal microbiome has been proposed to be involved in a range of diseases including the esophageal adenocarcinoma cascade; however, little is currently known about its function and relationship to the host. Here, the esophageal microbiomes of 106 prospectively recruited patients were assessed using 16S rRNA and 18S rRNA amplicon sequencing as well as shotgun sequencing, and associations with age, gender, proton pump inhibitor use, host genetics, and disease were tested. RESULTS: The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. While age was found to be a significant factor driving microbiome composition, bacterial signatures and functions such as enrichment with Gram-negative oral-associated bacteria and microbial lactic acid production were associated with the early stages of the esophageal adenocarcinoma cascade. Non-bacterial microbes such as archaea, Candida spp., and bacteriophages were also identified in low abundance in the esophageal microbiome. Specific host SNPs in NOTCH2, STEAP2-AS1, and NREP were associated with the composition of the esophageal microbiome in our cohort. CONCLUSIONS: This study provides the most comprehensive assessment of the esophageal microbiome to date and identifies novel signatures and host markers that can be investigated further in the context of esophageal adenocarcinoma development.

Experiment 1

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Subjects

Location of subjects

Australia

Host species Species from which microbiome was sampled. Contact us to have more species added.

Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology

Esophagus Gullet,Oesophagus,Esophagus,esophagus

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Esophageal adenocarcinoma adenocarcinoma - esophagus,adenocarcinoma of esophagus,adenocarcinoma of the esophagus,esophageal adenocarcinoma,esophagus adenocarcinoma,oesophageal adenocarcinoma,Esophageal adenocarcinoma

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Cluster 1

Group 1 name Corresponds to the case (exposed) group for case-control studies

Cluster 2

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. This group consists of esotypes that are dominated by Streptococcus (Streptococcus mitis/oralis/pneumoniae).

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)

2 months

Lab analysis

Sequencing type

16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene

Not specified

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance

Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).

relative abundances

Statistical test

LEfSe

Significance threshold p-value or FDR threshold used for differential abundance testing (if any)

0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?

No

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool

2

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

decreased

Simpson Estimator of species richness and species evenness: more weight on species evenness

decreased

Richness Number of species

decreased

Signature 1

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Source: Additional file 1, page 6

Description: The taxonomic differences across clusters in 16S rRNA amplicon data using LEfSe analysis.

Abundance in Group 1: increased abundance in Cluster 2

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Bacilli
Lactobacillales
Porphyromonas
Prevotella
Streptococcaceae
Streptococcus
unclassified Bacillales

Revision editor(s): Fiddyhamma, Victoria

Signature 2

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Source: Additional file 1, page 6

Description: The taxonomic differences across clusters in 16S rRNA amplicon data using LEfSe analysis.

Abundance in Group 1: decreased abundance in Cluster 2

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Prevotella

Revision editor(s): Fiddyhamma, Victoria

Experiment 2

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Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies

Cluster 3

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. This group consists of esotypes that are dominated by by Prevotella (Prevotella melaninogenica and Prevotella pallens), and to a lesser extent Veillonella.

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness

unchanged

Richness Number of species

unchanged

Signature 1

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Source: Additional file 1, page 6

Description: The taxonomic differences across clusters in 16S rRNA amplicon data using LEfSe analysis.

Abundance in Group 1: increased abundance in Cluster 3

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Actinomyces
Actinomycetaceae
Actinomycetales
Actinomycetota
Atopobium
Bacteroidales
Bacteroidia
Coriobacteriaceae
Coriobacteriales
Granulicatella
Kingella
Lachnoanaerobaculum
Lachnospiraceae
Megasphaera
Mogibacterium
Negativicutes
Prevotella
Prevotellaceae
Selenomonadales
Streptococcus
Veillonella
Veillonellaceae
unclassified Carnobacteriaceae
unclassified Lachnospiraceae
unclassified Veillonellaceae

Revision editor(s): Fiddyhamma, Victoria

Signature 2

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Source: Additional file 1, page 6

Description: The taxonomic differences across clusters in 16S rRNA amplicon data using LEfSe analysis.

Abundance in Group 1: decreased abundance in Cluster 3

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Prevotella

Revision editor(s): Fiddyhamma, Victoria

Experiment 3

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Cluster 2

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. This group consists of esotypes that are dominated by by Prevotella (Prevotella melaninogenica and Prevotella pallens), and to a lesser extent Veillonella.

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness

unchanged

Richness Number of species

unchanged

Signature 1

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Curated date: 2024/05/16

Curator: Fiddyhamma

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Source: Additional file 1, page 6

Description: The taxonomic differences across clusters in 16S rRNA amplicon data using LEfSe analysis.   

Abundance in Group 1: increased abundance in Cluster 3

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Actinomyces
Actinomycetaceae
Actinomycetales
Actinomycetota
Atopobium
Bacteroidales
Bacteroidia
Coriobacteriaceae
Coriobacteriales
Granulicatella
Kingella
Lachnoanaerobaculum
Lachnospiraceae
Megasphaera
Mogibacterium
Negativicutes
Prevotella
Prevotellaceae
Selenomonadales
Veillonella
Veillonellaceae
unclassified Carnobacteriaceae
unclassified Lachnospiraceae
unclassified Prevotellaceae
unclassified Veillonellaceae

Revision editor(s): Fiddyhamma, Victoria

Signature 2

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Source: Additional file 1, page 6

Description: The taxonomic differences across clusters in 16S rRNA amplicon data using LEfSe analysis.

Abundance in Group 1: decreased abundance in Cluster 3

NCBI	Quality Control	Links
Bacilli
Lactobacillales
Porphyromonas
Prevotella
Streptococcaceae
Streptococcus
unclassified Bacillales

Revision editor(s): Fiddyhamma, Victoria

Experiment 4

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Cluster 1

Group 1 name Corresponds to the case (exposed) group for case-control studies

Cluster 2

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. This group consists of esotypes that are dominated by Streptococcus (Streptococcus mitis/oralis/pneumoniae).

Lab analysis

Sequencing type

WMS

Statistical Analysis

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool

Not specified

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

decreased

Simpson Estimator of species richness and species evenness: more weight on species evenness

decreased

Richness Number of species

decreased

Signature 1

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Curated date: 2024/05/25

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Source: Additional file 1, page 7

Description: The taxonomic differences across clusters in MetaPhlan2 output from shotgun sequencing data using LEfSe analysis. 

Abundance in Group 1: increased abundance in Cluster 2

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Bacilli

Revision editor(s): Fiddyhamma, Victoria

Signature 2

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Source: Additional file 1, page 7

Description: The taxonomic differences across clusters in MetaPhlan2 output from shotgun sequencing data using LEfSe analysis.

Abundance in Group 1: decreased abundance in Cluster 2

NCBI	Quality Control	Links
Actinomycetales
Actinomycetota
Capnocytophaga
Flavobacteriaceae
Flavobacteriales
Flavobacteriia
Gammaproteobacteria
Haemophilus
Haemophilus parainfluenzae
Micrococcaceae
Pasteurellaceae
Pasteurellales
Pseudomonadota
Rothia
Rothia mucilaginosa
unclassified Granulicatella

Revision editor(s): Fiddyhamma, Victoria

Experiment 5

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Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies

Cluster 3

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. This group consists of esotypes that are dominated by by Prevotella (Prevotella melaninogenica and Prevotella pallens), and to a lesser extent Veillonella.

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness

unchanged

Richness Number of species

unchanged

Signature 1

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Curated date: 2024/05/29

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Source: Additional file 1, page 7

Description: The taxonomic differences across clusters in MetaPhlan2 output from shotgun sequencing data using LEfSe analysis.

Abundance in Group 1: increased abundance in Cluster 3

NCBI	Quality Control	Links
Bacteroidales
Bacteroidia
Negativicutes
Prevotella histicola
Prevotella pallens
Prevotella veroralis
Selenomonadales
Veillonella
Veillonellaceae
unclassified Veillonella

Revision editor(s): Fiddyhamma, Victoria

Signature 2

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Source: Additional file 1, page 7

Description: The taxonomic differences across clusters in MetaPhlan2 output from shotgun sequencing data using LEfSe analysis.   

Abundance in Group 1: decreased abundance in Cluster 3

NCBI	Quality Control	Links
Actinomycetales
Actinomycetota
Capnocytophaga
Flavobacteriaceae
Flavobacteriales
Flavobacteriia
Gammaproteobacteria
Haemophilus
Haemophilus parainfluenzae
Micrococcaceae
Pasteurellaceae
Pasteurellales
Pseudomonadota
Rothia
Rothia mucilaginosa
unclassified Granulicatella

Revision editor(s): Fiddyhamma, Victoria

Experiment 6

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Cluster 2

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness

unchanged

Richness Number of species

unchanged

Signature 1

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2024/05/29

Curator: Fiddyhamma

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Source: Additional file 1, page 7

Description: The taxonomic differences across clusters in MetaPhlan2 output from shotgun sequencing data using LEfSe analysis.

Abundance in Group 1: increased abundance in Cluster 3

NCBI	Quality Control	Links
Bacteroidales
Bacteroidia
Negativicutes
Prevotella histicola
Prevotella pallens
Prevotella veroralis
Selenomonadales
Veillonella
Veillonellaceae
unclassified Veillonella

Revision editor(s): Fiddyhamma, Victoria

Signature 2

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Source: Additional file 1, page 7

Description: The taxonomic differences across clusters in MetaPhlan2 output from shotgun sequencing data using LEfSe analysis.

Abundance in Group 1: decreased abundance in Cluster 3

NCBI	Quality Control	Links
Bacilli

Revision editor(s): Fiddyhamma, Victoria

Experiment 7

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Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Gastroesophageal reflux disease acid reflux,Esophageal Reflux,Gastresophageal reflux,Gastro Esophageal Reflux,Gastro oesophageal Reflux,Gastro-Esophageal Reflux,gastro-esophageal reflux,Gastro-oesophageal Reflux,Gastroesophageal Reflux,gastroesophageal reflux,GASTROESOPHAGEAL REFLUX DIS,gastroesophageal reflux disease,gastroesophageal reflux, pediatric,ger,GERD,GERD - gastro-esophageal reflux disease,Reflux, Gastro-Esophageal,Reflux, Gastro-oesophageal,Reflux, Gastroesophageal,Gastroesophageal reflux disease

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Normal (Normal esophagus)

Group 1 name Corresponds to the case (exposed) group for case-control studies

GERD (Gastroesophageal reflux disease)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

This group consists of patients with Gastroesophageal reflux disease.

Group 0 sample size Number of subjects in the control (unexposed) group

59

Group 1 sample size Number of subjects in the case (exposed) group

29

Lab analysis

Sequencing type

16S

Statistical Analysis

Signature 1

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Source: Additional file 3, page 4

Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).

Abundance in Group 1: increased abundance in GERD (Gastroesophageal reflux disease)

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Acetoanaerobium
Filifactor
unclassified Flavobacteriaceae
Campylobacter

Revision editor(s): Fiddyhamma, Victoria

Signature 2

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Revision editor(s): Victoria, Fiddyhamma

Source: Additional file 3, page 4

Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).

Abundance in Group 1: decreased abundance in GERD (Gastroesophageal reflux disease)

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Lactobacillus
Enterobacteriaceae
Enterobacterales
Escherichia/Shigella sp.

Revision editor(s): Victoria, Fiddyhamma

Experiment 8

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Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Normal

Group 1 name Corresponds to the case (exposed) group for case-control studies

Gastroesophageal reflux disease GERD(within subjects classified as PPI NO)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

This group consists of patients with Gastroesophageal reflux disease(within subjects classified as PPI NO)

Group 1 sample size Number of subjects in the case (exposed) group

19

Lab analysis

Statistical Analysis

Signature 1

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Source: Additional file 3, page 4

Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).

Abundance in Group 1: increased abundance in Gastroesophageal reflux disease GERD(within subjects classified as PPI NO)

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Rothia
Prevotella
unclassified Flavobacteriaceae
Streptococcus
Filifactor
Acetoanaerobium
unclassified Eubacteriales
Veillonella
Leptotrichia
Neisseriales
Neisseriaceae
Campylobacter
Cardiobacterium
unclassified Pasteurellaceae
Pseudomonadota incertae sedis

Revision editor(s): Fiddyhamma

Signature 2

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Source: Additional file 3, page 4

Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).

Abundance in Group 1: decreased abundance in Gastroesophageal reflux disease GERD(within subjects classified as PPI NO)

NCBI	Quality Control	Links
Slackia
Prevotella
Lactobacillus
unclassified Bacteroidales
Streptococcus
Oribacterium
Centipeda
Megasphaera
unclassified Veillonellaceae
Veillonella
Enterobacteriaceae
Escherichia/Shigella sp.
Enterobacterales

Revision editor(s): Fiddyhamma

Experiment 9

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Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Barrett's esophagus (ulcerative esophagitis) or (Barrett's esophagus),adenocarcinoma of esophagus,Barrett Epithelium,Barrett Esophagus,Barrett esophagus,Barrett metaplasia,Barrett Syndrome,Barrett's esophagus,Barrett's esophagus (disorder),Barrett's esophagus (disorder) [Ambiguous],Barrett's esophagus with esophagitis,Barrett's esophagus with esophagitis (disorder),Barrett's oesophagus,Barrett's Syndrome,Barrett's ulcer of esophagus,Barrett's ulcer of esophagus (disorder),Barretts Esophagus,Barretts syndrome,BE,cello,CLE,columnar epithelial-lined Lower esophagus,columnar-lined esophagus,Epithelium, Barrett,Esophagus, Barrett,Esophagus, Barrett's,Syndrome, Barrett,Syndrome, Barrett's,ulcerative esophagitis,barrett's esophagus

Group 1 name Corresponds to the case (exposed) group for case-control studies

Barrett’s Esophagus (BE)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

This group consists of patients with Barrett’s Esophagus

Group 1 sample size Number of subjects in the case (exposed) group

12

Lab analysis

Statistical Analysis

Signature 1

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Source: Additional file 3, page 4

Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).

Abundance in Group 1: increased abundance in Barrett’s Esophagus (BE)

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Leptotrichia
Capnocytophaga

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Experiment 10

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Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Gastroesophageal reflux disease (GERD)

Group 0 sample size Number of subjects in the control (unexposed) group

29

Lab analysis

Statistical Analysis

Signature 1

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Source: Additional file 3, page 4

Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).

Abundance in Group 1: increased abundance in Barrett’s Esophagus (BE)

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Burkholderiales
Capnocytophaga

Revision editor(s): Fiddyhamma

Signature 2

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Source: Additional file 3, page 4

Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).

Abundance in Group 1: decreased abundance in Barrett’s Esophagus (BE)

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Alloprevotella

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Experiment 11

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Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Esophageal adenocarcinoma adenocarcinoma - esophagus,adenocarcinoma of esophagus,adenocarcinoma of the esophagus,esophageal adenocarcinoma,esophagus adenocarcinoma,oesophageal adenocarcinoma,Esophageal adenocarcinoma

Group 1 name Corresponds to the case (exposed) group for case-control studies

Glandular mucosa (GM)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

This group consists of patients with Glandular mucosa

Group 1 sample size Number of subjects in the case (exposed) group

14

Lab analysis

Statistical Analysis

Signature 1

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Source: Additional file 3, page 4

Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).

Abundance in Group 1: increased abundance in Glandular mucosa (GM)

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Enterobacteriaceae
Enterobacterales
Prevotella
Saccharofermentans

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Signature 2

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Source: Additional file 3, page 4

Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).

Abundance in Group 1: decreased abundance in Glandular mucosa (GM)

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Prevotella
Acetoanaerobium
unclassified Prevotellaceae
unclassified Veillonellaceae

Revision editor(s): Fiddyhamma

Experiment 12

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Normal

Group 0 sample size Number of subjects in the control (unexposed) group

59

Lab analysis

Statistical Analysis

Signature 1

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Curated date: 2024/08/18

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Source: Additional file 3, page 4

Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).

Abundance in Group 1: increased abundance in Glandular mucosa (GM)

NCBI	Quality Control	Links
Prevotella
unclassified Prevotellaceae

Revision editor(s): Fiddyhamma

Signature 2

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Source: Additional file 3, page 4

Description: The differences across disease subgroups using LEfSe analysis (16S rRNA amplicon data).

Abundance in Group 1: decreased abundance in Glandular mucosa (GM)

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unclassified Prevotellaceae
unclassified Veillonellaceae

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Experiment 13

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Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Gastroesophageal reflux disease acid reflux,Esophageal Reflux,Gastresophageal reflux,Gastro Esophageal Reflux,Gastro oesophageal Reflux,Gastro-Esophageal Reflux,gastro-esophageal reflux,Gastro-oesophageal Reflux,Gastroesophageal Reflux,gastroesophageal reflux,GASTROESOPHAGEAL REFLUX DIS,gastroesophageal reflux disease,gastroesophageal reflux, pediatric,ger,GERD,GERD - gastro-esophageal reflux disease,Reflux, Gastro-Esophageal,Reflux, Gastro-oesophageal,Reflux, Gastroesophageal,Gastroesophageal reflux disease

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Normal (Normal esophagus)

Group 1 name Corresponds to the case (exposed) group for case-control studies

GERD (Gastroesophageal reflux disease)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

This group consists of patients with Gastroesophageal reflux disease.

Group 1 sample size Number of subjects in the case (exposed) group

29

Lab analysis

Sequencing type

WMS

Statistical Analysis

Signature 1

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Curator: Fiddyhamma

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Source: Additional file 3, page 5

Description: The differences across disease subgroups using LEfSe analysis (Shotgun MetaPhlan2 data).

Abundance in Group 1: increased abundance in GERD (Gastroesophageal reflux disease)

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Prevotella intermedia
Prevotella micans
Fusobacteriia
Fusobacteriales
Neisseria macacae
Neisseria meningitidis
Haemophilus parainfluenzae
Treponema medium

Revision editor(s): Fiddyhamma

Experiment 14

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Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies

GERD (Gastroesophageal reflux disease)within subjects classified as PPI NO

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

This group consists of patients with Gastroesophageal reflux disease(within subjects classified as PPI NO)

Group 1 sample size Number of subjects in the case (exposed) group

19

Lab analysis

Statistical Analysis

Signature 1

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Source: Additional file 3, page 5

Description: The differences across disease subgroups using LEfSe analysis (Shotgun MetaPhlan2 data).

Abundance in Group 1: increased abundance in GERD (Gastroesophageal reflux disease)within subjects classified as PPI NO

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Neisseria meningitidis

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Signature 2

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Source: Additional file 3, page 5

Description: The differences across disease subgroups using LEfSe analysis (Shotgun MetaPhlan2 data).

Abundance in Group 1: decreased abundance in GERD (Gastroesophageal reflux disease)within subjects classified as PPI NO

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Megasphaera micronuciformis
Megasphaera
Prevotella pallens
rothia unclassifiedrothia unclassified

Revision editor(s): Fiddyhamma

Experiment 15

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Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Barrett's esophagus (ulcerative esophagitis) or (Barrett's esophagus),adenocarcinoma of esophagus,Barrett Epithelium,Barrett Esophagus,Barrett esophagus,Barrett metaplasia,Barrett Syndrome,Barrett's esophagus,Barrett's esophagus (disorder),Barrett's esophagus (disorder) [Ambiguous],Barrett's esophagus with esophagitis,Barrett's esophagus with esophagitis (disorder),Barrett's oesophagus,Barrett's Syndrome,Barrett's ulcer of esophagus,Barrett's ulcer of esophagus (disorder),Barretts Esophagus,Barretts syndrome,BE,cello,CLE,columnar epithelial-lined Lower esophagus,columnar-lined esophagus,Epithelium, Barrett,Esophagus, Barrett,Esophagus, Barrett's,Syndrome, Barrett,Syndrome, Barrett's,ulcerative esophagitis,barrett's esophagus

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Normal

Group 1 name Corresponds to the case (exposed) group for case-control studies

Barrett’s Esophagus (BE)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

This group consists of patients with Barrett’s Esophagus

Group 1 sample size Number of subjects in the case (exposed) group

12

Lab analysis

Statistical Analysis

Signature 1

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Source: Additional file 3, page 5

Description: The differences across disease subgroups using LEfSe analysis (Shotgun MetaPhlan2 data).

Abundance in Group 1: increased abundance in Barrett’s Esophagus (BE)

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unclassified Gemella
Streptococcus sanguinis
Veillonella sp. oral taxon 780

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Experiment 16

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Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Esophageal adenocarcinoma adenocarcinoma - esophagus,adenocarcinoma of esophagus,adenocarcinoma of the esophagus,esophageal adenocarcinoma,esophagus adenocarcinoma,oesophageal adenocarcinoma,Esophageal adenocarcinoma

Group 1 name Corresponds to the case (exposed) group for case-control studies

Glandular mucosa (GM)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

This group consists of patients with Glandular mucosa

Group 1 sample size Number of subjects in the case (exposed) group

14

Lab analysis

Statistical Analysis

Signature 1

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Source: Additional file 3, page 5

Description: The differences across disease subgroups using LEfSe analysis (Shotgun MetaPhlan2 data).

Abundance in Group 1: increased abundance in Glandular mucosa (GM)

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Abiotrophia
Abiotrophia defectiva
Aerococcaceae
Anaeroglobus
Anaeroglobus geminatus
Burkholderia
Deltaproteobacteria
Desulfobacterales
Desulfobulbaceae
Desulfobulbus
Desulfobulbus sp. oral taxon 041
Eggerthia
Eggerthia catenaformis
Fusobacterium necrophorum
Helicobacter
Helicobacter pylori
Helicobacteraceae
Hoylesella oralis
Neisseria cinerea
Neisseria flavescens
Prevotella multiformis
Streptococcus australis
Streptococcus gordonii
Treponema socranskii
unclassified Burkholderia
Bacteroidetes bacterium oral taxon 272Bacteroidetes bacterium oral taxon 272

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Experiment 17

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

GERD(Gastroesophageal reflux disease)

Group 0 sample size Number of subjects in the control (unexposed) group

29

Lab analysis

Statistical Analysis

Signature 1

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Curated date: 2024/09/24

Curator: Fiddyhamma

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Source: Additional file 3, page 5

Description: The differences across disease subgroups using LEfSe analysis (Shotgun MetaPhlan2 data).

Abundance in Group 1: increased abundance in Glandular mucosa (GM)

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Abiotrophia
Abiotrophia defectiva
Aerococcaceae
Aggregatibacter aphrophilus
Eggerthia
Eggerthia catenaformis
Fusobacterium necrophorum
Helicobacter
Helicobacter pylori
Helicobacteraceae
Hoylesella oralis
Kingella
Neisseria cinerea
Porphyromonas gingivalis
Selenomonas noxia
Streptococcus gordonii
unclassified Kingella (in: b-proteobacteria)
Bacteroidetes bacterium oral taxon 272Bacteroidetes bacterium oral taxon 272

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Experiment 18

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Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Gastroesophageal reflux disease acid reflux,Esophageal Reflux,Gastresophageal reflux,Gastro Esophageal Reflux,Gastro oesophageal Reflux,Gastro-Esophageal Reflux,gastro-esophageal reflux,Gastro-oesophageal Reflux,Gastroesophageal Reflux,gastroesophageal reflux,GASTROESOPHAGEAL REFLUX DIS,gastroesophageal reflux disease,gastroesophageal reflux, pediatric,ger,GERD,GERD - gastro-esophageal reflux disease,Reflux, Gastro-Esophageal,Reflux, Gastro-oesophageal,Reflux, Gastroesophageal,Gastroesophageal reflux disease

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Normal (Cluster 1)

Group 1 name Corresponds to the case (exposed) group for case-control studies

GERD(Gastroesophageal reflux disease) (Cluster 1)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

This group consists of patients with Gastroesophageal reflux disease.

Group 0 sample size Number of subjects in the control (unexposed) group

Not specified

Group 1 sample size Number of subjects in the case (exposed) group

Not specified

Lab analysis

Sequencing type

16S

Statistical Analysis

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool

2

Signature 1

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Source: Additional file 3, page 6

Description: Differences across normal subjects and GERD patients in each clusters using LEfSe analysis

Abundance in Group 1: increased abundance in GERD(Gastroesophageal reflux disease) (Cluster 1)

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unclassified Flavobacteriaceae
Streptococcus
Veillonella

Revision editor(s): Fiddyhamma

Signature 2

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Curator: Fiddyhamma

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Source: Additional file 3, page 6

Description: Differences across normal subjects and GERD patients in each clusters using LEfSe analysis

Abundance in Group 1: decreased abundance in GERD(Gastroesophageal reflux disease) (Cluster 1)

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Lactobacillus
Enterobacteriaceae
Enterobacterales

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Experiment 19

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Normal (Cluster 2)

Group 1 name Corresponds to the case (exposed) group for case-control studies

GERD(Gastroesophageal reflux disease) (Cluster 2)

Lab analysis

Statistical Analysis

Signature 1

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Source: Additional file 3, page 6

Description: Differences across normal subjects and GERD patients in each clusters using LEfSe analysis

Abundance in Group 1: increased abundance in GERD(Gastroesophageal reflux disease) (Cluster 2)

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Corynebacterium
unclassified Actinomycetales
Prevotella
Oribacterium
Filifactor
Erysipelotrichia
Erysipelotrichales
Erysipelotrichaceae
Solobacterium
Selenomonas
Veillonella
Leptotrichiaceae
Brachymonas
Neisseria
unclassified Pasteurellaceae
unclassified Bacillota

Revision editor(s): Fiddyhamma

Signature 2

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Source: Additional file 3, page 6

Description: Differences across normal subjects and GERD patients in each clusters using LEfSe analysis

Abundance in Group 1: decreased abundance in GERD(Gastroesophageal reflux disease) (Cluster 2)

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Prevotella
Gammaproteobacteria
Pasteurellales
Pasteurellaceae
unclassified Pasteurellaceae

Revision editor(s): Fiddyhamma

Experiment 20

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Normal (Cluster 3)

Group 1 name Corresponds to the case (exposed) group for case-control studies

GERD(Gastroesophageal reflux disease) (Cluster 3)

Lab analysis

Statistical Analysis

Signature 1

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Source: Additional file 3, page 6

Description: Differences across normal subjects and GERD patients in each clusters using LEfSe analysis

Abundance in Group 1: increased abundance in GERD(Gastroesophageal reflux disease) (Cluster 3)

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Prevotella
Flavobacteriia
Flavobacteriales
Flavobacteriaceae
Capnocytophaga
unclassified Flavobacteriaceae
unclassified Pseudomonadaceae
unclassified Bacillota

Revision editor(s): Fiddyhamma

Signature 2

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Source: Additional file 3, page 6

Description: Differences across normal subjects and GERD patients in each clusters using LEfSe analysis

Abundance in Group 1: decreased abundance in GERD(Gastroesophageal reflux disease) (Cluster 3)

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Peptostreptococcaceae
unclassified sequences

Revision editor(s): Fiddyhamma

Experiment 21

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Normal (Cluster 1)

Group 1 name Corresponds to the case (exposed) group for case-control studies

GERD(Gastroesophageal reflux disease) (Cluster 1)

Lab analysis

Sequencing type

WMS

Statistical Analysis

Signature 1

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Curated date: 2024/09/24

Curator: Fiddyhamma

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Source: Additional file 3, page 7

Description: Differences across normal subjects and GERD patients in each clusters using LEfSe analysis

Abundance in Group 1: increased abundance in GERD(Gastroesophageal reflux disease) (Cluster 1)

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Alloprevotella tannerae
unclassified Alloprevotella
Eubacteriaceae
Eubacterium

Revision editor(s): Fiddyhamma

Signature 2

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Source: Additional file 3, page 7

Description: Differences across normal subjects and GERD patients in each clusters using LEfSe analysis

Abundance in Group 1: decreased abundance in GERD(Gastroesophageal reflux disease) (Cluster 1)

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Alloprevotella

Revision editor(s): Fiddyhamma

Experiment 22

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Normal (Cluster 2)

Group 1 name Corresponds to the case (exposed) group for case-control studies

GERD(Gastroesophageal reflux disease) (Cluster 2)

Lab analysis

Statistical Analysis

Signature 1

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Source: Additional file 3, page 7

Description: Differences across normal subjects and GERD patients in each clusters using LEfSe analysis

Abundance in Group 1: increased abundance in GERD(Gastroesophageal reflux disease) (Cluster 2)

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Actinomycetales
Actinomycetota
Bacteria
Eubacteriales Family XIII. Incertae Sedis
Leptotrichia
Leptotrichia wadei
Leptotrichiaceae
Micrococcaceae
Prevotella denticola
Prevotella nigrescens
Rothia mucilaginosa
Segatella oris
Streptococcus salivarius
Streptococcus vestibularis
[Eubacterium] infirmum
unclassified Leptotrichia
Clostridiales Family XIII incertae sedis nonameClostridiales Family XIII incertae sedis noname
Rothia

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Signature 2

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Source: Additional file 3, page 7

Description: Differences across normal subjects and GERD patients in each clusters using LEfSe analysis

Abundance in Group 1: decreased abundance in GERD(Gastroesophageal reflux disease) (Cluster 2)

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Haemophilus parahaemolyticus

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Experiment 23

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Normal (Cluster 3)

Group 1 name Corresponds to the case (exposed) group for case-control studies

GERD(Gastroesophageal reflux disease) (Cluster 3)

Lab analysis

Statistical Analysis

Signature 1

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Curator: Fiddyhamma

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Source: Additional file 3, page 7

Description: Differences across normal subjects and GERD patients in each clusters using LEfSe analysis

Abundance in Group 1: increased abundance in GERD(Gastroesophageal reflux disease) (Cluster 3)

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Bacillales
Gammaproteobacteria
Gemella
Haemophilus
Haemophilus parainfluenzae
Neisseria
Neisseria macacae
Neisseria meningitidis
Neisseriaceae
Neisseriales
Pasteurellales
Pasteuriaceae
Pseudomonadota
Treponema medium
unclassified Bacillales

Revision editor(s): Fiddyhamma

Signature 2

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Source: Additional file 3, page 7

Description: Differences across normal subjects and GERD patients in each clusters using LEfSe analysis

Abundance in Group 1: decreased abundance in GERD(Gastroesophageal reflux disease) (Cluster 3)

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Prevotellaceae
Bacteroidales
Bacteroidia
Atopobium
Coriobacteriaceae
Prevotella
Coriobacteriales
Lancefieldella parvula

Revision editor(s): Fiddyhamma

Experiment 24

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Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Esophageal adenocarcinoma adenocarcinoma - esophagus,adenocarcinoma of esophagus,adenocarcinoma of the esophagus,esophageal adenocarcinoma,esophagus adenocarcinoma,oesophageal adenocarcinoma,Esophageal adenocarcinoma

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Subjects with normal esophagus on PPI-No

Group 1 name Corresponds to the case (exposed) group for case-control studies

Subjects with normal esophagus on PPI-Yes

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

This group consists of patients with normal esophagus

Lab analysis

Sequencing type

16S

Statistical Analysis

Signature 1

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Source: Additional figure 3 A

Description: Microbial taxa identified using LEfSe analysis to be differentially abundant between subjects on PPI as compared to subjects not on PPI

Abundance in Group 1: increased abundance in Subjects with normal esophagus on PPI-Yes

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Prevotella dentalis
Streptococcus vestibularis

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Signature 2

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Source: Additional figure 3A

Description: Microbial taxa identified using LEfSe analysis to be differentially abundant between subjects on PPI as compared to subjects not on PPI

Abundance in Group 1: decreased abundance in Subjects with normal esophagus on PPI-Yes

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Peptostreptococcus
Haemophilus influenzae
Segatella salivae

Revision editor(s): Fiddyhamma

Experiment 25

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Subjects with GERD on PPI-No

Group 1 name Corresponds to the case (exposed) group for case-control studies

Subjects with GERD on PPI-Yes

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

This group consists of patients with gastroesophageal reflux disease

Lab analysis

Statistical Analysis

Signature 1

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Source: Additional figure 3A

Description: Microbial taxa identified using LEfSe analysis to be differentially abundant between subjects on PPI as compared to subjects not on PPI

Abundance in Group 1: increased abundance in Subjects with GERD on PPI-Yes

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Actinomyces graevenitzii
unclassified Rothia (in: high G+C Gram-positive bacteria)
Alloprevotella
Prevotella histicola
Prevotella pallens
Segatella salivae
Gemella morbillorum
Streptococcus constellatus
Lachnospiraceae
Stomatobaculum
Stomatobaculum longum
Negativicutes
Selenomonadales
Veillonellaceae
Megasphaera
Megasphaera micronuciformis
Veillonella

Revision editor(s): Fiddyhamma

Signature 2

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Source: Additional figure 3A

Description: Microbial taxa identified using LEfSe analysis to be differentially abundant between subjects on PPI as compared to subjects not on PPI

Abundance in Group 1: decreased abundance in Subjects with GERD on PPI-Yes

NCBI	Quality Control	Links
Neisseria meningitidis

Revision editor(s): Fiddyhamma